Contacts of the helix formed by residues 486 - 497 (chain 5) in PDB entry 5U8T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 486 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6322 SER* 3.3 40.3 + - - +
4425 LYS* 4.3 8.2 + - - +
4485 GLY* 3.0 28.1 - - - -
4495 LEU* 3.0 23.2 - - + +
4505 THR* 3.4 9.3 + - - +
4525 SER* 5.3 5.2 - - - -
4845 LYS 3.6 1.2 + - - -
4855 MET* 1.3 74.4 - - + +
4875 ASP* 1.3 54.9 + - - +
4885 GLU* 3.1 23.4 + - - +
4895 ASP* 2.3 41.5 + - - +
4905 ARG* 2.7 36.2 + - - +
11F T 3.9 21.2 + - - -
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Residues in contact with ASP 487 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4773 LYS* 5.9 0.2 - - - +
4855 MET 3.3 5.7 - - - +
4865 ARG* 1.3 73.5 - - - +
4885 GLU* 1.3 65.9 + - - +
4905 ARG* 3.1 44.1 + - - +
4915 VAL* 3.9 9.7 + - - +
5415 ASP* 3.8 6.1 - - - +
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Residues in contact with GLU 488 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4353 ARG* 3.1 53.3 + - - +
4865 ARG* 3.1 35.6 + - - +
4875 ASP* 1.3 84.4 + - - +
4895 ASP* 1.3 65.6 + - + +
4905 ARG 3.3 0.2 - - - -
4915 VAL* 3.6 9.0 - - - +
11F T 4.8 4.3 + - - -
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Residues in contact with ASP 489 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4353 ARG* 4.4 5.6 - - - +
4495 LEU* 4.4 7.1 - - - +
4505 THR* 2.7 32.2 + - + +
4855 MET* 5.0 1.2 - - - +
4865 ARG* 2.3 61.3 + - - +
4885 GLU* 1.3 81.4 - - + +
4905 ARG* 1.3 61.0 + - - +
4915 VAL 2.9 1.3 - - - -
4925 ALA* 2.8 25.5 + - + +
4935 ILE* 2.9 17.5 + - - +
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Residues in contact with ARG 490 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4825 PHE* 3.2 38.4 + - - -
4835 ASP* 4.2 11.7 + - - +
4855 MET* 3.5 34.7 + - + +
4865 ARG 2.7 22.3 + - - +
4875 ASP* 3.1 31.6 + - - +
4895 ASP* 1.3 76.9 - - - +
4915 VAL* 1.3 57.5 + - + +
4935 ILE* 3.2 6.6 + - - +
4945 HIS* 2.8 49.4 + - + +
5405 ILE* 4.0 7.1 - - - +
5415 ASP* 2.5 49.7 + - - +
5435 GLN* 5.5 1.6 - - - +
5465 ILE* 5.0 1.6 - - - +
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Residues in contact with VAL 491 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4333 THR* 5.7 5.2 - - - +
4353 ARG* 4.2 7.0 - - - +
4743 GLU* 3.3 38.6 - - + -
4773 LYS* 3.6 32.1 - - + -
4875 ASP 4.0 9.9 - - - +
4885 GLU* 3.6 14.6 + - - +
4895 ASP 2.9 0.2 - - - -
4905 ARG* 1.3 74.4 - - + +
4925 ALA* 1.3 60.0 + - - +
4935 ILE 3.0 1.6 - - - -
4945 HIS* 2.9 36.0 + - + +
4955 GLU* 2.9 17.5 + - + +
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Residues in contact with ALA 492 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4333 THR* 5.1 7.2 - - - +
4353 ARG* 5.7 4.5 - - + +
4505 THR* 3.5 21.1 - - + -
4885 GLU 4.2 0.4 + - - -
4895 ASP* 2.8 23.5 + - + +
4915 VAL* 1.3 78.9 - - - +
4935 ILE* 1.3 58.3 + - - +
4955 GLU* 3.8 9.2 - - - +
4965 ALA* 2.9 32.2 + - - +
5025 ILE* 4.1 18.8 - - + +
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Residues in contact with ILE 493 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4495 LEU* 3.5 34.3 - - + -
4505 THR* 4.8 3.4 - - + -
4695 MET* 3.7 26.9 - - + -
4795 ILE* 5.1 5.6 - - + -
4825 PHE* 4.7 7.4 - - + -
4855 MET* 3.6 26.5 - - + -
4895 ASP 2.9 11.0 + - - +
4905 ARG 3.2 8.5 - - - +
4915 VAL 3.0 0.2 - - - -
4925 ALA* 1.3 80.0 - - - +
4945 HIS* 1.3 57.5 + - - +
4955 GLU 2.9 10.5 + - - -
4965 ALA* 4.7 5.2 - - + -
4975 MET* 2.9 55.7 + - + +
5195 VAL* 4.9 4.0 - - + -
5505 PHE* 5.3 0.2 - - + -
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Residues in contact with HIS 494 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4743 GLU* 5.6 1.5 - - - +
4773 LYS* 5.6 1.3 - - - -
10013 ANP 4.6 7.1 + - - -
4825 PHE* 5.0 4.0 - + - -
4855 MET* 5.2 0.4 - - + -
4905 ARG* 2.8 45.4 + - + +
4915 VAL* 2.9 34.3 + - + +
4935 ILE* 1.3 76.8 - - - +
4955 GLU* 1.3 53.7 + - - +
4975 MET* 4.1 3.0 - - - +
4985 GLU* 2.8 18.4 - - - +
5435 GLN* 3.4 18.1 + - - -
5465 ILE* 3.6 35.4 - - + +
5495 ARG* 3.0 53.7 + - - +
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Residues in contact with GLU 495 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4203 ARG* 3.6 6.4 + - - -
4333 THR* 3.4 31.5 + - + +
4733 ASP* 3.3 26.0 - - - +
4743 GLU* 6.0 1.8 - - + +
10013 ANP 5.6 0.7 - - - +
4915 VAL* 3.2 16.6 - - + +
4925 ALA* 3.9 6.2 - - - +
4935 ILE 2.9 2.6 - - - -
4945 HIS* 1.3 78.2 - - - +
4965 ALA* 1.3 54.4 + - - +
4975 MET 3.1 1.3 - - - -
4985 GLU* 2.8 8.9 + - - -
4995 GLN* 2.7 51.2 + - + +
5015 THR* 2.7 45.7 + - - +
5025 ILE* 3.5 11.1 - - - +
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Residues in contact with ALA 496 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4695 MET* 5.9 1.8 - - + -
4925 ALA 2.9 21.8 + - - +
4935 ILE* 4.7 7.6 - - + -
4955 GLU* 1.3 73.6 - - - +
4975 MET* 1.3 65.3 + - - +
5005 GLN* 3.2 21.4 - - - +
5015 THR 3.0 20.2 - - - +
5025 ILE* 3.6 9.6 - - + -
5155 SER* 3.0 31.6 - - - +
5175 THR* 4.8 4.1 - - - +
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Residues in contact with MET 497 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4075 ARG* 3.0 26.7 + - - +
4115 ASN* 3.9 12.3 + - - +
4935 ILE* 2.9 44.2 - - + +
4945 HIS* 4.1 5.2 - - - +
4955 GLU 3.1 0.8 - - - -
4965 ALA* 1.3 78.6 - - + +
4985 GLU* 1.3 80.0 + - - +
5005 GLN* 3.9 4.5 - - - +
5175 THR* 4.7 10.2 - - - +
5195 VAL* 3.4 24.5 - - + -
5465 ILE* 5.9 0.2 - - + -
5495 ARG* 3.6 22.4 - - + +
5505 PHE* 3.3 33.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il